Abstract
Near isogenic F2 (NIF2) population frequently developed by conventional backcross has dramatically contributed to QTL identification in plants. Developing such a NIF2 population is time-consuming. Thus, it is urgent to rapidly produce a NIF2 population for QTL cloning. Here, we proposed a rapid QTL cloning strategy by generating a Pseudo-near isogenic F2 population (Pseudo-NIF2), which segregates at the target QTL but is fixed at other QTLs for the target trait. Nineteen QTLs for GL, GW, and TGW were detected in the F2 population from the cross between Zhenshan 97 and Egy316. To verify the efficiency of Pseudo-NIF2 in QTL quick cloning, the novel moderate QTL qGL10.1 which explained 9.1% and 5.6% of grain length variation in F2 and F2:3 populations was taken as an example. An F2 plant (F2-120), which segregated at qGL10.1 but fixed at other 8 QTLs for grain length, was screened to generate a Pseudo-NIF2 population by selfing cross. In the Pseudo-NIF2 population, the segregation ratio of plants with long grains to short grains fits 3:1, indicating that one gene controlled the variation of grain length. Based on the Pseudo-NIF2 and its progeny, qGL10.1 was fine mapped to a 19.3-kb region, where a gene OsMADS56 was verified as the candidate by functional polymorphism between parental alleles. Pseudo-NIF2 strategy is a rapid way for QTL cloning, which saves 3 to 4 cropping seasons compared to the conventional way. Applying the method for cloning QTL with moderate or major effects is promising.
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The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.
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Acknowledgements
The authors thank Mr. JB. Wang for his outstanding fieldwork in managing the field experiments.
Funding
This work is partially supported by the National Natural Science Foundation of China (32061143042), and a bilateral project entitled “mapping of early heading and yield-related trait genes in Chinese and Egyptian rice resources” between Benha University and Huazhong Agricultural University. The Talented Young Scientists Program China 2019 (TYSP).
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Sherif A wrote the paper. Sherif A, Zhang B, Wu B, Hu Y, Li S, and Zhou X conducted all experiments and analyzed the data. Ayaad M and Hassan IO developed the Egyptian mutant (Egy316). Ayaad M, El-Badri AM, El-Badawy MEM, Sedhom SA, and Abo-Yousef M developed the F2 population. Xing YZ designed, guided this study, and revised the paper.
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Sherif, A., Zhang, B., Wu, B. et al. A Pseudo-near isogenic F2 population strategy for rapid QTL cloning. Mol Breeding 43, 61 (2023). https://doi.org/10.1007/s11032-023-01408-x
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DOI: https://doi.org/10.1007/s11032-023-01408-x